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This study quantified Escherichia coli (E.coli) for 511 self-supply sources and at point-of-use for 173 households in the cities of Bekasi and Metro. A structured questionnaire collected information about the household, water sources and potential on-site contamination sources. Univariate and multivariate logistic regression analysis examined risk factors for faecal contamination. E.coli was detected in 66% of sources, including 55% of boreholes, 64% of protected dug wells and 82% of unprotected dug wells. Widespread boiling of water meant microbial quality improved significantly between source and point-of-use, with E.coli detected in 30% of self-supply samples at point-of-use. Unprotected dug wells were significantly more likely to be contaminated than boreholes. In Bekasi, the analysis found a significant association between presence of E.coli and sanitation systems located within 10m of the groundwater source. 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